ABSTRACT Alcohol and nicotine are the most commonly abused legal drugs in the United States. There is a high incidence of nicotine dependence in alcohol-dependent individuals, and there is also high rate of problem drinking in habitual smokers. There is considerable overlap in the patterns of use and, in particular, misuse of these drugs, suggesting that common mechanisms of action may underlie alcohol and nicotine co-dependence. The combined health consequences of alcohol and nicotine co-dependence represent not only a serious health threat to millions, but also create an enormous burden on health care systems worldwide. We will utilize state of the art next generation sequencing (ABI SOLiD technology) to profile transcriptional regulation in human brain regions that are known substrates of reward circuitry involved in the development of alcohol and nicotine dependence. An understanding of gene expression changes resulting from alcohol and nicotine abuse (and the resulting phenotypes) may identify novel targets for the development of new treatments and provide a rationale for treatment and prevention strategies. We hypothesize that long-term alcohol and nicotine use and abuse results in changes in gene expression in brain and that these changes are responsible, at least partly, for co- dependence of these drugs. Three Specific Aims are proposed: 1) utilize next generation transcriptome profiling (RNA-seq) to identify differentially expressed RNAs in select brain regions of well-characterized alcohol-dependent cases that have documented smoking histories compared to matched controls, 2) confirm expression differences in select gene using targeted transcript sequencing, and 3) targeted transcript sequencing will be used to identify precise genes and expressed sequence variants in the frontal cortex and amygdala that have been implicated in genome-wide and candidate gene association studies of alcohol and nicotine dependence. PUBLIC HEALTH RELEVANCE: The overall goal of this proposal is to utilize next generation sequencing to discover novel genes that may be involved in alcohol and nicotine co-dependence. Gene expression will be examined in post-mortem human brain regions that are thought to be involved in the rewarding properties of drugs of abuse.